Iron in PDB 7rtq: Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide

The structure of Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide, PDB code: 7rtq was solved by G.I.Lepesheva, T.Y.Hargrove, Z.Wawrzak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	64.63 / 2.11
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	75.062, 75.223, 105.953, 89.49, 74.63, 63.98
R / Rfree (%)	21.1 / 23.7

The structure of Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide also contains other interesting chemical elements:

Fluorine

(F)

24 atoms

The binding sites of Iron atom in the Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide (pdb code 7rtq). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide, PDB code: 7rtq:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:10.0 occ:1.00 FE A:HEM501 0.0 10.0 1.0 ND A:HEM501 1.9 9.9 1.0 NA A:HEM501 2.0 10.4 1.0 N21 A:7PW502 2.0 17.8 0.4 N21 A:7PW502 2.0 16.0 0.6 NC A:HEM501 2.1 10.9 1.0 NB A:HEM501 2.1 8.7 1.0 SG A:CYS430 2.3 13.8 1.0 C4D A:HEM501 2.9 9.0 1.0 C1D A:HEM501 2.9 10.0 1.0 C1A A:HEM501 2.9 10.7 1.0 C11 A:7PW502 3.0 19.7 0.4 C11 A:7PW502 3.0 17.9 0.6 C4A A:HEM501 3.0 11.4 1.0 C10 A:7PW502 3.1 20.1 0.4 C4C A:HEM501 3.1 10.9 1.0 C1B A:HEM501 3.1 8.8 1.0 C10 A:7PW502 3.1 18.4 0.6 C4B A:HEM501 3.1 9.2 1.0 C1C A:HEM501 3.1 10.9 1.0 CB A:CYS430 3.3 13.6 1.0 CHA A:HEM501 3.3 10.0 1.0 CHD A:HEM501 3.4 9.6 1.0 CHB A:HEM501 3.5 9.7 1.0 CHC A:HEM501 3.5 9.2 1.0 CA A:CYS430 4.0 12.8 1.0 N33 A:7PW502 4.1 20.4 0.4 N33 A:7PW502 4.1 18.4 0.6 C9 A:7PW502 4.1 20.9 0.4 C2A A:HEM501 4.1 10.4 1.0 C3D A:HEM501 4.2 10.9 1.0 C2D A:HEM501 4.2 10.9 1.0 C9 A:7PW502 4.2 18.9 0.6 C3A A:HEM501 4.2 10.9 1.0 C3C A:HEM501 4.3 12.0 1.0 C2C A:HEM501 4.3 11.0 1.0 C2B A:HEM501 4.3 9.0 1.0 C3B A:HEM501 4.4 9.4 1.0 N A:GLY432 4.7 12.8 1.0 C A:CYS430 4.8 13.7 1.0 N A:ILE431 4.9 13.2 1.0 CA A:GLY432 5.0 12.6 1.0

Iron binding site 2 out of 4 in the Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe501 b:9.2 occ:1.00 FE B:HEM501 0.0 9.2 1.0 ND B:HEM501 1.9 10.7 1.0 NA B:HEM501 2.0 8.9 1.0 N21 B:7PW502 2.0 15.1 0.4 N21 B:7PW502 2.0 13.1 0.6 NC B:HEM501 2.1 11.0 1.0 NB B:HEM501 2.1 9.0 1.0 SG B:CYS430 2.3 11.0 1.0 C4D B:HEM501 2.9 10.7 1.0 C1D B:HEM501 2.9 11.2 1.0 C1A B:HEM501 3.0 9.6 1.0 C11 B:7PW502 3.0 15.5 0.4 C10 B:7PW502 3.0 17.0 0.6 C4A B:HEM501 3.0 10.4 1.0 C11 B:7PW502 3.0 13.5 0.6 C10 B:7PW502 3.1 18.6 0.4 C4C B:HEM501 3.1 11.5 1.0 C1B B:HEM501 3.1 9.8 1.0 C4B B:HEM501 3.1 9.7 1.0 C1C B:HEM501 3.1 11.0 1.0 CB B:CYS430 3.3 9.7 1.0 CHA B:HEM501 3.3 10.5 1.0 CHD B:HEM501 3.4 10.7 1.0 CHB B:HEM501 3.5 9.8 1.0 CHC B:HEM501 3.5 9.9 1.0 CA B:CYS430 4.0 10.2 1.0 N33 B:7PW502 4.1 16.8 0.4 C2D B:HEM501 4.1 10.9 1.0 C3D B:HEM501 4.2 11.7 1.0 C9 B:7PW502 4.2 17.7 0.4 C9 B:7PW502 4.2 15.8 0.6 C2A B:HEM501 4.2 10.1 1.0 N33 B:7PW502 4.2 14.5 0.6 C3A B:HEM501 4.2 10.4 1.0 C3C B:HEM501 4.3 12.4 1.0 C2C B:HEM501 4.3 11.4 1.0 C2B B:HEM501 4.3 9.1 1.0 C3B B:HEM501 4.4 9.9 1.0 N B:GLY432 4.7 12.0 1.0 C B:CYS430 4.8 11.9 1.0 N B:ILE431 4.9 12.4 1.0 CA B:GLY432 5.0 13.0 1.0

Iron binding site 3 out of 4 in the Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe501 b:10.6 occ:1.00 FE C:HEM501 0.0 10.6 1.0 ND C:HEM501 1.9 12.6 1.0 NA C:HEM501 2.0 10.2 1.0 N21 C:7PW502 2.0 15.9 0.6 N21 C:7PW502 2.0 18.2 0.4 NC C:HEM501 2.1 12.2 1.0 NB C:HEM501 2.1 10.6 1.0 SG C:CYS430 2.3 13.1 1.0 C4D C:HEM501 2.9 12.6 1.0 C1D C:HEM501 2.9 13.0 1.0 C10 C:7PW502 2.9 20.3 0.4 C10 C:7PW502 2.9 18.3 0.6 C1A C:HEM501 3.0 11.7 1.0 C11 C:7PW502 3.0 18.8 0.6 C4A C:HEM501 3.0 10.9 1.0 C4C C:HEM501 3.0 12.4 1.0 C11 C:7PW502 3.1 20.8 0.4 C1B C:HEM501 3.1 11.1 1.0 C4B C:HEM501 3.1 10.9 1.0 C1C C:HEM501 3.1 12.8 1.0 CB C:CYS430 3.2 12.0 1.0 CHA C:HEM501 3.3 12.7 1.0 CHD C:HEM501 3.4 12.3 1.0 CHB C:HEM501 3.5 10.7 1.0 CHC C:HEM501 3.5 11.4 1.0 CA C:CYS430 3.9 11.6 1.0 C9 C:7PW502 4.1 20.7 0.4 C9 C:7PW502 4.1 18.6 0.6 N33 C:7PW502 4.1 17.8 0.6 N33 C:7PW502 4.1 20.4 0.4 C2D C:HEM501 4.2 12.5 1.0 C3D C:HEM501 4.2 13.3 1.0 C2A C:HEM501 4.2 11.6 1.0 C3A C:HEM501 4.2 11.5 1.0 C3C C:HEM501 4.3 13.4 1.0 C2C C:HEM501 4.3 13.7 1.0 C2B C:HEM501 4.3 10.8 1.0 C3B C:HEM501 4.4 11.1 1.0 N C:GLY432 4.7 14.4 1.0 C C:CYS430 4.8 13.4 1.0 N C:ILE431 4.9 13.9 1.0 CA C:GLY432 5.0 14.8 1.0

Iron binding site 4 out of 4 in the Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Sterol 14ALPHA Demethylase (CYP51) From Naegleria Fowleri in Complex with An Inhibitor R)-N-(1-(3,4'-Difluorobiphenyl-4-Yl)-2-(1H- Imidazol-1-Yl)Ethyl)-4-(5-Phenyl-1,3,4-Oxadiazol-2-Yl)Benzamide within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe501 b:9.8 occ:1.00 FE D:HEM501 0.0 9.8 1.0 ND D:HEM501 1.9 9.1 1.0 NA D:HEM501 2.0 8.2 1.0 N21 D:7PW502 2.1 17.8 0.4 N21 D:7PW502 2.1 15.2 0.6 NC D:HEM501 2.1 9.1 1.0 NB D:HEM501 2.1 8.2 1.0 SG D:CYS430 2.3 12.4 1.0 C4D D:HEM501 2.9 8.6 1.0 C11 D:7PW502 2.9 20.1 0.4 C1D D:HEM501 2.9 9.1 1.0 C1A D:HEM501 3.0 9.2 1.0 C11 D:7PW502 3.0 17.8 0.6 C4A D:HEM501 3.0 10.1 1.0 C4C D:HEM501 3.1 10.1 1.0 C1B D:HEM501 3.1 8.7 1.0 C4B D:HEM501 3.1 8.5 1.0 C1C D:HEM501 3.1 10.0 1.0 C10 D:7PW502 3.1 18.0 0.6 C10 D:7PW502 3.2 20.8 0.4 CB D:CYS430 3.3 11.5 1.0 CHA D:HEM501 3.3 9.2 1.0 CHD D:HEM501 3.4 8.9 1.0 CHB D:HEM501 3.5 9.5 1.0 CHC D:HEM501 3.5 8.6 1.0 CA D:CYS430 4.0 12.2 1.0 N33 D:7PW502 4.1 22.2 0.4 N33 D:7PW502 4.1 19.4 0.6 C2D D:HEM501 4.2 8.9 1.0 C3D D:HEM501 4.2 10.1 1.0 C2A D:HEM501 4.2 10.3 1.0 C3A D:HEM501 4.2 10.4 1.0 C9 D:7PW502 4.2 19.6 0.6 C9 D:7PW502 4.2 22.2 0.4 C3C D:HEM501 4.3 11.8 1.0 C2C D:HEM501 4.3 10.9 1.0 C2B D:HEM501 4.3 9.5 1.0 C3B D:HEM501 4.4 9.2 1.0 N D:GLY432 4.7 14.0 1.0 C D:CYS430 4.9 13.2 1.0 N D:ILE431 4.9 13.2 1.0 CA D:GLY432 5.0 14.2 1.0

T.Hargrove, Z.Wawrzak, G.Rachakonda, W.Nes, F.Villalta, F.Guengerich, G.Lepesheva. Relaxed Substrate Requirements of Sterol 14ALPHA-Demethylase From Naegleria Fowleri Are Accompanied By Resistance to Inhibition J.Med.Chem. 2021.
ISSN: ISSN 0022-2623